Laiwu pigs, distinguished by their high intramuscular fat of 7–9%, is an indigenous pig breed of China, and recent studies also found that Laiwu pigs showed high resistance to Porcine circovirus type 2. However, with the introduction of commercial varieties, the population of Laiwu pigs has declined, and some lineages have disappeared, which could result in inbreeding. Runs of homozygosity (ROH) can be used as a good measure of individual inbreeding status and is also normally used to detect selection signatures so as to map the candidate genes associated with economically important traits. In this study, we used data from Genotyping by Genome Reducing and Sequencing to investigate the number, length, coverage, and distribution patterns of ROH in 93 Chinese Laiwu pigs and identified genomic regions with a high ROH frequency. The average inbreeding coefficient calculated by pedigree was 0.021, whereas that estimated by all detected ROH segments was 0.133. Covering 13.4% of the whole genome, a total of 7,508 ROH segments longer than 1 Mb were detected, whose average length was 3.76 Mb, and short segments (1–5 Mb) dominated. For individuals, the coverage was in the range between 0.56 and 36.86%. For chromosomes, SSC6 had the largest number (n = 688), and the number of ROH in SSC12 was the lowest (n = 215). Thirteen ROH islands were detected in our study, and 86 genes were found within those regions. Some of these genes were correlated with economically important traits, such as meat quality (ECI1, LRP12, NDUFA4L2, GIL1, and LYZ), immunity capacity (IL23A, STAT2, STAT6, TBK1, IFNG, and ITH2), production (DCSTAMP, RDH16, and GDF11), and reproduction (ODF1 and CDK2). A total of six significant Gene Ontology terms and nine significant Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified, most of which were correlated with disease resistance and biosynthesis processes, and one KEGG pathway was related to lipid metabolism. In addition, we aligned all of the ROH islands to the pig quantitative trait loci (QTL) database and finally found eight QTL related to the intramuscular fat trait. These results may help us understand the characteristics of Laiwu pigs and provide insight for future breeding strategies.

Hu sheep, a famous breed in the Taihu Basin, has the advantages of non-seasonal estrus, multiple fetuses, coarse feeding tolerance, and suitability for house feeding. Runs of homozygosity (ROHs) were found to be an effective tool to detect the animal population structure and economic traits. The detection of ROHs is beneficial for reducing the incidence of inbreeding as well as identifying harmful variants in the genome. However, there is a lack of systemic reports on ruminants in previous studies of ROHs. Here, we sequenced 108 Hu sheep, detected ROHs in Hu sheep to calculate their inbreeding coefficient, and selected genes of Hu sheep breeds within the ROH islands which are relevant to agricultural economic characteristics. Then, we compared the characteristics of the occurrences of SNPs between Hu sheep and other sheep breeds, and also investigated the distribution of the frequencies of SNPs within specific gene regions of Hu sheep breeds to select their breed-specific genes. Furthermore, we performed a comparative genome and transcriptome analysis in human and sheep breeds to identify important reproduction-related genes. In this way, we found some significant SNPs, and mapped these with a set of interesting candidate genes which are related to the productive value of livestock (FGF9, BMPR1B, EFNB3, MICU2, GFRA3), healthy characteristics (LGSN, EPHA5, ALOX15B), and breed specificity (FGF9, SAP18, MICU2). These results in our study describe various production traits of Hu sheep from a genetic perspective, and provide insights into the genetic management and complementary understanding of Hu sheep.

In Chinese pig populations in which crossbreeding is used, these animals show a level of weakness compared with their original purebred ancestors. For instance, in the Lulai pig, a newly developed Chinese breed that is raised on the basis of the Laiwu pig (a Chinese indigenous breed with exceptionally high intramuscular fat content) and the Yorkshire pig using a method of systematic crossbreeding, both their market acceptance and performance are inferior. To reveal the practical role of these admixed breeds and traditional systematic crossbreeding methods at the genomic level, we explored population structure, genetic signatures, and introgression. We conducted this study based on the SNP chip data of 381 Lulai pigs, 182 Laiwu pigs, and 127 Yorkshires, which showed deficient genome coverage during our study. Therefore, we further selected the Genotyping by Genome Reducing and Sequencing (GGRS) method, which has a high density and suitable genome coverage as a supplement. We applied the GGRS data of 38 Lulai pigs, 75 Laiwu pigs, and 75 Yorkshires. In terms of the SNP chip data, by Fst analysis, we detected 782 significantly different genes between Lulai pigs and Yorkshires, including 3 major genes associated with growth (LEPR) and meat quality (SCD and TBC1D1), and we detected 426 significantly different genes between Lulai pigs and Laiwu pigs. With rIBD, we detected 12 genomic regions that included 182 genes that Yorkshires introgressed to Lulai pigs, and we detected 27 genomic regions that included 229 genes with a major gene (SCD) that Laiwu pigs introgressed to Lulai pigs. Regarding the GGRS data, we detected 601 significantly different genes between Lulai pigs and Yorkshires by Fst analysis, including 3 major genes associated with growth and fat deposits (IGF2 and FTO) and with hair color (KIT), and we detected 634 significantly different genes between Lulai pigs and Laiwu pigs, including 3 major genes related to their body composition (MYPN), hair color (KIT), and ear size (PPARD). By rIBD, we detected 94 deep sections that included 363 genes that Yorkshires introgressed to Lulai pigs, and we detected 149 deep sections that included 727 genes with a major gene (ESR1) that Laiwu pigs introgressed to Lulai pigs. Altogether, this study provides both insight into the molecular background of synthesized breeds of Lulai pigs and a reference for the evaluation of systematic crossbreeding in China.

Excessive fat deposition can trigger metabolic diseases, and it is crucial to identify factors that can break the link between fat deposition and metabolic diseases. Healthy obese Laiwu pigs (LW) are high in fat content but resistant to metabolic diseases. In this study, we compared the fecal microbiome, fecal and blood metabolome, and genome of LW and Lulai pigs (LU) to identify factors that can block the link between fat deposition and metabolic diseases. Our results show significant differences in Spirochetes and Treponema, which are involved in carbohydrate metabolism, between LW and LU. The fecal and blood metabolome composition was similar, and some anti-metabolic disease components of blood metabolites were different between the two breeds of pigs. The predicted differential RNA is mainly enriched in lipid metabolism and glucose metabolism, which is consistent with the functions of differential microbiota and metabolites. The down-regulated gene RGP1 is strongly negatively correlated with Treponema. Our omics data would provide valuable resources for further scientific research on healthy obesity in both human and porcine.